There is an option in Thunderbird, tools, account setting, servers settings, to leave messages that are downloaded from your server to Thunderbird. Not knowing who your server is, you may have those same options from him, to leave downloaded messages online for whatever options they offer. If you did not have either of these settings to have emails remain, and have deleted them, then yes, they are gone. You always have had the option to move emails to another folder in Thunderbird also. I leave them in the "drafts" folder, if I am not ready to send them, and have made personal folders to retain received messages I wish to keep permanently.